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Research Article | Host-Microbe Biology

American Gut: an Open Platform for Citizen Science Microbiome Research

Daniel McDonald, Embriette Hyde, Justine W. Debelius, James T. Morton, Antonio Gonzalez, Gail Ackermann, Alexander A. Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C. Dorrestein, Robert R. Dunn, Ashkaan K. Fahimipour, James Gaffney, Jack A. Gilbert, Grant Gogul, Jessica L. Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A. Jackson, Stefan Janssen, Dilip V. Jeste, Lingjing Jiang, Scott T. Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V. Melnik, Jessica L. Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T. Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S. Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D. Swafford, Varykina G. Thackray, Luke R. Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, The American Gut Consortium, Rob Knight
Casey S. Greene, Editor
Daniel McDonald
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Embriette Hyde
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Justine W. Debelius
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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James T. Morton
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Antonio Gonzalez
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Gail Ackermann
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Alexander A. Aksenov
bCollaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA
cSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
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Bahar Behsaz
dDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
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Caitriona Brennan
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Yingfeng Chen
eDepartment of Biology, San Diego State University, San Diego, California, USA
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Lindsay DeRight Goldasich
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Pieter C. Dorrestein
bCollaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA
cSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
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Robert R. Dunn
fDepartment of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
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Ashkaan K. Fahimipour
gBiology and the Built Environment Center, University of Oregon, Eugene, Oregon, USA
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James Gaffney
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Jack A. Gilbert
hDepartment of Surgery, University of Chicago, Chicago, Illinois, USA
iInstitute for Genomic and Systems Biology, University of Chicago, Chicago, Illinois, USA
jDepartment of Biosciences, Argonne National Laboratory, Chicago, Illinois, USA
kMarine Biology Laboratory, University of Chicago, Chicago, Illinois, USA
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Grant Gogul
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Jessica L. Green
gBiology and the Built Environment Center, University of Oregon, Eugene, Oregon, USA
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Philip Hugenholtz
lAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, the University of Queensland, Brisbane, QLD, Australia
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Greg Humphrey
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Curtis Huttenhower
mHarvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
nThe Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Matthew A. Jackson
oDepartment of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
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Stefan Janssen
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Dilip V. Jeste
pDepartments of Psychiatry and Neurosciences, University of California San Diego, La Jolla, California, USA
qSam and Rose Stein Institute for Research on Aging and Center for Healthy Aging, University of California San Diego, La Jolla, California, USA
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Lingjing Jiang
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Scott T. Kelley
eDepartment of Biology, San Diego State University, San Diego, California, USA
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Dan Knights
rDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
sBiotechnology Institute, University of Minnesota, Minneapolis, Minnesota, USA
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Tomasz Kosciolek
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Joshua Ladau
tThe Gladstone Institutes, University of California, San Francisco, California, USA
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Jeff Leach
uHuman Food Project, Terlingua, Texas, USA
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Clarisse Marotz
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Dmitry Meleshko
vSt. Petersburg State University, Center for Algorithmic Biotechnology, Saint Petersburg, Russia
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Alexey V. Melnik
bCollaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA
cSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
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Jessica L. Metcalf
wDepartment of Animal Science, Colorado State University, Fort Collins, Colorado, USA
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Hosein Mohimani
xDepartment of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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Emmanuel Montassier
rDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
yUniversité de Nantes, Microbiotas Hosts Antibiotics and Bacterial Resistances (MiHAR), Nantes, France
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Jose Navas-Molina
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Tanya T. Nguyen
pDepartments of Psychiatry and Neurosciences, University of California San Diego, La Jolla, California, USA
qSam and Rose Stein Institute for Research on Aging and Center for Healthy Aging, University of California San Diego, La Jolla, California, USA
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Shyamal Peddada
zDepartment of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Pavel Pevzner
bCollaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA
dDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
aaCenter for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
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Katherine S. Pollard
tThe Gladstone Institutes, University of California, San Francisco, California, USA
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Gholamali Rahnavard
mHarvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
nThe Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Adam Robbins-Pianka
bbDepartment of Computer Science, University of Colorado Boulder, Boulder, Colorado, USA
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Naseer Sangwan
jDepartment of Biosciences, Argonne National Laboratory, Chicago, Illinois, USA
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Joshua Shorenstein
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Larry Smarr
dDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
aaCenter for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
ccCalifornia Institute for Telecommunications and Information Technology (Calit2), University of California San Diego, La Jolla, California, USA
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Se Jin Song
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Timothy Spector
oDepartment of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
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Austin D. Swafford
aaCenter for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
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Varykina G. Thackray
ddDepartment of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
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Luke R. Thompson
eeOcean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
ffDepartment of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA
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Anupriya Tripathi
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Yoshiki Vázquez-Baeza
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Alison Vrbanac
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Paul Wischmeyer
ggDepartment of Anesthesiology and Surgery, Duke University School of Medicine, Durham, North Carolina, USA
hhDuke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA
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Elaine Wolfe
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Qiyun Zhu
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
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Rob Knight
aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
dDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
aaCenter for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
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Casey S. Greene
University of Pennsylvania
Roles: Editor
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DOI: 10.1128/mSystems.00031-18
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Article Information

DOI 
https://doi.org/10.1128/mSystems.00031-18

Published By 
American Society for Microbiology Journals
History 
  • Received March 8, 2018
  • Accepted April 16, 2018
  • Published online May 15, 2018.

Copyright & Usage 
Copyright © 2018 McDonald et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Editors and / or Reviewers 
  • Casey S. Greene, Editor, University of Pennsylvania

Author Information

  1. Daniel McDonalda,
  2. Embriette Hydea,
  3. Justine W. Debeliusa,
  4. James T. Mortona,
  5. Antonio Gonzaleza,
  6. Gail Ackermanna,
  7. Alexander A. Aksenovb,c,
  8. Bahar Behsazd,
  9. Caitriona Brennana,
  10. Yingfeng Chene,
  11. Lindsay DeRight Goldasicha,
  12. Pieter C. Dorresteinb,c,
  13. Robert R. Dunnf,
  14. Ashkaan K. Fahimipourg,
  15. James Gaffneya,
  16. Jack A. Gilberth,i,j,k,
  17. Grant Gogula,
  18. Jessica L. Greeng,
  19. Philip Hugenholtzl,
  20. Greg Humphreya,
  21. Curtis Huttenhowerm,n,
  22. Matthew A. Jacksono,
  23. Stefan Janssena,
  24. Dilip V. Jestep,q,
  25. Lingjing Jianga,
  26. Scott T. Kelleye,
  27. Dan Knightsr,s,
  28. Tomasz Koscioleka,
  29. Joshua Ladaut,
  30. Jeff Leachu,
  31. Clarisse Marotza,
  32. Dmitry Meleshkov,
  33. Alexey V. Melnikb,c,
  34. Jessica L. Metcalfw,
  35. Hosein Mohimanix,
  36. Emmanuel Montassierr,y,
  37. Jose Navas-Molinaa,
  38. Tanya T. Nguyenp,q,
  39. Shyamal Peddadaz,
  40. Pavel Pevznerb,d,aa,
  41. Katherine S. Pollardt,
  42. Gholamali Rahnavardm,n,
  43. Adam Robbins-Piankabb,
  44. Naseer Sangwanj,
  45. Joshua Shorensteina,
  46. Larry Smarrd,aa,cc,
  47. Se Jin Songa,
  48. Timothy Spectoro,
  49. Austin D. Swaffordaa,
  50. Varykina G. Thackraydd,
  51. Luke R. Thompsonee,ff,
  52. Anupriya Tripathia,
  53. Yoshiki Vázquez-Baezaa,
  54. Alison Vrbanaca,
  55. Paul Wischmeyergg,hh,
  56. Elaine Wolfea,
  57. Qiyun Zhua,
  58. The American Gut Consortium and
  59. Rob Knighta,d,aa
  1. aDepartment of Pediatrics, University of California San Diego, La Jolla, California, USA
  2. bCollaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA
  3. cSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
  4. dDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
  5. eDepartment of Biology, San Diego State University, San Diego, California, USA
  6. fDepartment of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
  7. gBiology and the Built Environment Center, University of Oregon, Eugene, Oregon, USA
  8. hDepartment of Surgery, University of Chicago, Chicago, Illinois, USA
  9. iInstitute for Genomic and Systems Biology, University of Chicago, Chicago, Illinois, USA
  10. jDepartment of Biosciences, Argonne National Laboratory, Chicago, Illinois, USA
  11. kMarine Biology Laboratory, University of Chicago, Chicago, Illinois, USA
  12. lAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, the University of Queensland, Brisbane, QLD, Australia
  13. mHarvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
  14. nThe Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
  15. oDepartment of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
  16. pDepartments of Psychiatry and Neurosciences, University of California San Diego, La Jolla, California, USA
  17. qSam and Rose Stein Institute for Research on Aging and Center for Healthy Aging, University of California San Diego, La Jolla, California, USA
  18. rDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
  19. sBiotechnology Institute, University of Minnesota, Minneapolis, Minnesota, USA
  20. tThe Gladstone Institutes, University of California, San Francisco, California, USA
  21. uHuman Food Project, Terlingua, Texas, USA
  22. vSt. Petersburg State University, Center for Algorithmic Biotechnology, Saint Petersburg, Russia
  23. wDepartment of Animal Science, Colorado State University, Fort Collins, Colorado, USA
  24. xDepartment of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
  25. yUniversité de Nantes, Microbiotas Hosts Antibiotics and Bacterial Resistances (MiHAR), Nantes, France
  26. zDepartment of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
  27. aaCenter for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
  28. bbDepartment of Computer Science, University of Colorado Boulder, Boulder, Colorado, USA
  29. ccCalifornia Institute for Telecommunications and Information Technology (Calit2), University of California San Diego, La Jolla, California, USA
  30. ddDepartment of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
  31. eeOcean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
  32. ffDepartment of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA
  33. ggDepartment of Anesthesiology and Surgery, Duke University School of Medicine, Durham, North Carolina, USA
  34. hhDuke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA
  • Address correspondence to Rob Knight, robknight{at}ucsd.edu.
  • D. McDonald and E. Hyde contributed equally to this work.

  • Citation McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, The American Gut Consortium, Knight R. 2018. American Gut: an open platform for citizen science microbiome research. mSystems 3:e00031-18. https://doi.org/10.1128/mSystems.00031-18.

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American Gut: an Open Platform for Citizen Science Microbiome Research
Daniel McDonald, Embriette Hyde, Justine W. Debelius, James T. Morton, Antonio Gonzalez, Gail Ackermann, Alexander A. Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C. Dorrestein, Robert R. Dunn, Ashkaan K. Fahimipour, James Gaffney, Jack A. Gilbert, Grant Gogul, Jessica L. Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A. Jackson, Stefan Janssen, Dilip V. Jeste, Lingjing Jiang, Scott T. Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V. Melnik, Jessica L. Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T. Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S. Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D. Swafford, Varykina G. Thackray, Luke R. Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, The American Gut Consortium, Rob Knight
mSystems May 2018, 3 (3) e00031-18; DOI: 10.1128/mSystems.00031-18

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American Gut: an Open Platform for Citizen Science Microbiome Research
Daniel McDonald, Embriette Hyde, Justine W. Debelius, James T. Morton, Antonio Gonzalez, Gail Ackermann, Alexander A. Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C. Dorrestein, Robert R. Dunn, Ashkaan K. Fahimipour, James Gaffney, Jack A. Gilbert, Grant Gogul, Jessica L. Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A. Jackson, Stefan Janssen, Dilip V. Jeste, Lingjing Jiang, Scott T. Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V. Melnik, Jessica L. Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T. Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S. Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D. Swafford, Varykina G. Thackray, Luke R. Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, The American Gut Consortium, Rob Knight
mSystems May 2018, 3 (3) e00031-18; DOI: 10.1128/mSystems.00031-18
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    • ABSTRACT
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KEYWORDS

citizen science
microbiome

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